Congenital kidney malformations are the leading cause of chronic renal failure in children. At present, we have a poor understanding of the developmental pathways that control the formation of the nephron, the key functional unit of the kidney. We are using zebrafish to elucidate the embryonic pathways that govern the subdivision of the nephron into functionally distinct segments. The zebrafish embryo is ideal for these studies as the intermediate mesoderm on either side of the trunk forms two simple linear nephrons. From a functional genomics approach we have isolated a number of renal transcription factor and solute transporter genes. The expression patterns of these genes subdivide the zebrafish nephron into distinct proximal and distal segments much like the mammalian nephron. Combinations of transcription factors define each segment suggesting a `renal transcription factor code'determines segment identity. This code is disrupted in embryos deficient in the homeobox transcription factor genes cdx1a and cdx4, which act as master regulators of the hox genes. Doubly-deficient embryos display abnormal hox expression patterns, a posterior shift in the position of the kidney, and a loss of distal tubules. In addition, cdx mutants exhibit expanded expression of Wilms'tumor suppressor-1a (wt1a), a transcription factor implicated in metanephros development and podocyte differentiation in mammals. The cdx genes are expressed in the trunk (paraxial mesoderm) adjacent to the intermediate mesoderm. Expression of raldh2, encoding an enzyme involved in retinoic acid (RA) synthesis, is expanded in the paraxial mesoderm of cdx-deficient embryos. Knock-down of Raldh2 in cdx4 mutants is able to rescue the kidney positioning defect, whereas in wild-types it down-regulates wt1a expression. These results suggest that aberrant RA signaling is responsible for the renal defects in cdx mutants and led us to examine the role of RA in nephron segmentation. Using DEAB, a chemical antagonist of Raldh2, we found that RA is required at multiple stages of nephrogenesis to induce podocytes and the proximal tubules, and to suppress distal tubule fates. Based on these data we hypothesize that the cdx-hox pathway acts upstream of raldh2 to restrict RA synthesis and that RA induces podocytes and proximal tubule fates by up-regulating genes such as wt1a. The aims of this proposal are designed to test this hypothesis. We will characterize the cellular and molecular nephron defects in cdx- and RA-deficient animals and use rescue experiments and knock-down studies to determine the epistatic relationships between the cdx, hox, and raldh2 genes. Using chemical and molecular antagonists of RA, as well as a RA-responsive transgenic reporter line, we will determine where and when RA signaling is required to induce proximal nephron fates. These studies will establish a link between the cdx-hox and RA pathways in the control of nephron segmentation, shed new light on renal birth defects, and will be useful for developing new therapies to treat, or prevent, chronic renal failure.Birth defects that affect the kidneys are the leading cause of chronic renal failure in infants and children, however at present, we have a poor understanding of the genes that control kidney formation. We have found that retinoic acid, a derivative of Vitamin A, plays a central role in regulating normal renal development. This work advances our understanding of how kidneys arise in the embryo and may be lead to new therapeutic targets to treat or prevent chronic renal failure.